Superoxide Dismutase





Superoxide dismutase (SOD) are a group of antioxidant enzymes which catalyze the dismutation of superoxide to oxygen and hydrogen peroxide. SODs are critical antioxidative proteins, protecting the host from oxidative damage.

Types of SOD:
SOD uses metals as cofactors and are named accordingly: Cu-Zn-SOD, Cu-SOD, Fe-SOD, Mn-SOD. The Cu-Zn-SOD is most commonly found in eukaryotes, including humans, while Fe-SOD and Mn-SOD are found in prokaryotes. Mn-SOD is also found in eukaryotes (see 2adq and Nitrotyrosine). The 2D and 3D images above are of a Human Cu-Zn-SOD with copper and zinc metal ions visible.



Structure:


The structure of SOD was first solved by Irwin Fridovich and Joe McCord in 1973, with the structure of human-like Cu-ZN SOD solved soon after by Richardson et al. The typical SOD structure is an 8-stranded “Greek Key” beta-barrel with an active site buried between the barrel and two surface loops. While the typical biological unit for SOD is either dimmer or tetramer, monomer forms exist, such as the bovine SOD at the right. The Image at the left by Dr. Jane Richardson, illustrates the Greek-Key structure and position of the metal cations.

Biochemistry
Superoxide is a highly reactive oxygen species and is a major source of oxidative stress in the body, reacting with cellular targets, often causing oxidative damage. SOD protects the body by safely metabolizing the superoxide into unreactive oxygen and hydrogen peroxide. Experiments conducted with knockout mice unable to produce SOD develop widespread oxidative damage and hepatocarcinogenesis and exhibit a greatly reduced lifespan. In humans, mutations to SOD1, one of 3 types found in the human body, can cause familial ALS, a motor neuron disease better known as Lou Gherig’s Disease, and has also been linked to Down’s Syndrome.

Additional Resources
See: Copper, Zinc Superoxide Dismutase

3D Structures of SOD
Update June 2011

Metal-free apo SOD
3hog – SOD – tomato

1p7g – SOD – Pyrobaculum aerophilum

1ozt, 3gzp, 3gzq, 3ecv, 3ecw, 2gbu - hSOD (mutant) - human

3ecu, 3k91 – hSOD

1rk7 - hSOD (mutant) – NMR

3kbe – CeSOD – Caenorhabditis elegans

1t6i, 1t6q – ScSOD - Streptomyces coelicolor

3ak1 - ApSOD - Aeropyrum pernix

Cu-Zn-SOD
2jlp, 2v0a, 2c9v, 2c9u, 2c9s, 1pu0, 1hl5, 1sos, 1spd, 3kh3, 3kh4 - hSOD +Zn+Cu - human

3h2p, 3h2q, 3h2r, 3hff, 3gqf, 2nnx, 1p1v, 1oez, 2xjl, 3qqd – hSOD (mutant) +Zn

2af2, 1kmg - hSOD (mutant) +Zn – NMR

1l3n, 1dsw, 1ba9 – hSOD (mutant) +Zn+Cu - NMR

2wyz - hSOD (mutant) +Zn+Cu+UMP

2wz0 - hSOD (mutant) +Zn+Cu+aniline

2wz5 - hSOD (mutant) +Zn+Cu+methionine

2wz6 - hSOD (mutant) +Zn+Cu+quinazoline

2r27 - hSOD +Cu

1hl4 - hSOD +Zn

2wko, 3gzo, 2zkw, 2zkx, 2zky, 3cqp, 3cqq, 2vr6, 2vr7, 2vr8, 2gbt, 2gbv, 1uxl, 1uxm, 1ptz, 1ozu, 1n18, 1n19, 1fun, 1mfm, 1azv, 2wyt, 2xjk – hSOD (mutant) +Zn+Cu

3l9e - smSOD +Zn – silk moth

3l9y - smSOD +Zn+Cu

2wn0, 2wwn, 2wwo – YpSOD+Zn+Cu – Yersinia pseudotuberculosis

2wn1 - YpSOD+Zn+Cu+N3

2z7u, 2z7w, 2z7y, 2z7z, 2aeo, 1q0e, 1e9p, 1e9q, 1cb4, 1cbj, 1sxn, 1sxa, 1sxb, 1sxc, 1spd, 1sda, 3sod, 2sod, 2zow, 3hw7 – cSOD+Zn+Cu - cow

1cob – cSOD+Cu+Co

1sxs - cSOD +Zn+Cu+SCN

1sxz - cSOD +Zn+Cu+N3

1e9o – cSOD+Cu

3f7k - ApSOD +Zn+Cu+H2O2 – Alvinella pompejana

3f7l - ApSOD +Zn+Cu

2k4w – SeSOD (mutant) +Zn+Cu – Salmonella enterica – NMR

1eqw - SOD +Zn+Cu – Salmonella typhimurium

3ce1 - SOD +Zn+Cu – Cryptococcus liquefaciens

2q2l - SOD +Zn – Potentilla atrosanguinea

2aqm - SOD +Zn+Cu – Brucella abortus

2aps - SOD +Zn+Cu – Actinobacillus pleuropneumoniae

2aqn - NmSOD +Zn+Cu – Neisseria meningitides

2aqp, 2aqq, 2aqr, 2aqs, 2aqt – NmSOD (mutant) +Zn+Cu

1z9n - HdSOD +Zn+Cu+haem – Haemophilus ducreyi

1z9p - HdSOD +Zn+Cu

1to4, 1to5 - SOD +Zn+Cu – Schistosoma mansoni

1pzs - MtSOD +Cu – Mycobacterium tuberculosis

1oaj, 1bzo, 1yai - PlSOD +Zn+Cu – Photobacterium leiognathi

1oal, 1ib5, 1ibb, 1ibd, 1ibf, 1ibh – PlSOD (mutant) +Zn+Cu

1f18, 1f1a, 1f1d, 1b4t – ySOD (mutant) +Zn+Cu – yeast

1f1g, 1b4l, 2jcw, 1sdy - ySOD +Zn+Cu

1yaz - ySOD +Zn+Cu+N3

1jk9 – ySOD+Zn+Cu chaperone for SOD

1eso - EcSOD +Zn+Cu - Escherichia coli

1yso - EcSOD +Zn+Cu

1srd – SOD+MZn+Cu –Spinach

3gtt – mSOD+Zn – mouse

3gtv, 3ltv – mSOD/hSOD+Zn chimera

3kbf – CeSOD+Zn+Cu

3km1, 3km2 – tSOD+Zn

3mkg – SOD + Zn - tomato

Mn-SOD
Human Mn-SOD is discussed in the article on Nitrotyrosine.

3k9s – EcSOD+H2O2

1d5n, 1vew, 3ot7 - EcSOD+Mn

1zlz, 1ixb, 1ix9, 1en4, 1en5, 1en6, 1i08, 1i0h – EcSOD (mutant)+Mn

3dc5, 3dc6 – SOD+Mn – Caenorhabditis elegans

3bfr, 1jcv, 3lsu – ySOD+Mn

2qka, 2adp, 2adq, 1xdc, 1xil, 1n0j, 1luv, 1msd – hSOD+Mn

2qkc, 3c3s, 3c3t, 2p4k, 1zsp, 1zte, 1zuq, 2gds, 1szx, 1pl4, 1pm9, 1n0n, 1luw, 1ja8, 1em1, 1ap5, 1ap6, 1qnm, 1var – hSOD (mutant)+Mn

2rcv – SOD+Mn – Bacillus subtilis

1xre, 1xuq – SOD+Mn – Bacillus anthracis

2aw9, 2cdy, 2ce4, 3kky – DrSOD+Mn – Deinococcus radiodurans

2a03 – SOD+Mn+Zn – Plasmodium berghei

1jr9 - SOD +Zn+Mn – Virgibacillus halodenitrificans

1gv3 – SOD+Mn – Anabaena

1kkc – SOD+Mn – Aspergillus fumigatus

1xso – SOD+Mn – Xenopus laevis

1mng, 3mds – TtSOD+Mn – Thermus thermophilus

3evk – SOD+Mn – Pyrobaculum aerophilum

1ar4, 1ar5 – PfSOD+Mn - Propionibacterium freudenreichii

3ak2 - ApSOD+Mn

Fe-SOD
3js4 – SOD+Fe – Anaplasma phagocytuphilum

1mmm – EcSOD+Fe

1y67 – DrSOD+Fe

3esf – SOD (mutant)+Fe – Trypanosoma brucei

2gpc – SOD+Fe – Trypanosoma cruzi

3h1s – SOD+Fe – Francisella tularensis

2w7w – SOD+Fe – Aliivibrio salmonicida

3cei – SOD+Fe – Helicobacter pylori

2goj, 2bpi – PfSOD+Fe – Plasmodium falciparum

2awp – SOD+ion – Plasmodium knowlesi

2bkb, 2nyb, 1za5 – EcSOD (mutant)+Fe

2cw2, 2cw3 – SOD+Fe – Perkinsus marinus

1wb7, 1wb8 – SOD (mutant)+Fe – Sulfolobus solfataricus

1unf – SOD+Fe – Vigna unguiculata

1uer, 1ues, 1qnn – SOD+Fe – Porphyromonas gingivalis

1my6 – SOD+Fe – Thermosynechococcus elongates

1ma1 – SOD+Fe – Methanothermobacter thermautotrophicus

1gn2, 1gn3, 1gn4, 1gn6 – MtSOD (mutant)+Fe

1ids – MtSOD+Fe

1dt0, 3sdp – SOD+Fe – Pseudomonas putida

1b06 – SOD+Fe – Sulfolobus acidocaldarius

1bs3 – PfSOD+Fe+F

1bsm, 1bt8 – PfSOD+Fe

1avm – PfSOD+Fe+N3

1coj – SOD+Fe – Aquifex pyrophilus

1isa, 1isb, 1isc – EcSOD+Fe

3lio, 3ljt, 3lj9, 3ljf – SOD+Fe

3ak3 - ApSOD+Fe

Ni-SOD
3g4x, 3g4z, 3g50, 1t6u – ScSOD (mutant)+Ni

1q0d, 1q0f, 1q0g, 1q0k, 1q0m – SOD+Ni – Streptomyces seoulensis